Introduction: In high-fat diet-induced obesity, the levels of cathepsin L (CTSL) and cathepsin B (CTSB) increase in adipocytes, resulting in insulin resistance in the adipose tissue. In this study, the preventive effect of endurance training on the gene expression of CTSL and CTSB was investigated in the adipose tissue of mice with a high-fat diet. Materials and Methods: Twenty-one male mice (age: four weeks, weight: 12 g) were assigned to three groups, including control (n=7), high-fat diet (HFD) (n=7), and endurance training/high-fat diet (ET-HFD) (n=7). The mice of the HFD group were fed HFD (42% fat) for 12 weeks. The mice in the ET-HFD group, along with HFD feeding, were submitted to continuous endurance training on a treadmill for six weeks (five sessions per week), with a progressive increase in intensity and volume. The real-time polymerase chain reaction (PCR) assay was used to assess the gene expression of CTSL and CTSB. Results: The HFD was fattening (P=0.001). The gene expression of CTSL did not significantly change in the groups (P=0.118). However, the gene expression of CTSB increased fivefold in the HFD group as compared to the control group (P=0.001). The increase in the level of CTSB was 50% lower in the ET-HFD group compared to the HFD group (P=0.013). Conclusion: Endurance training could partially prevent the upregulation of CTSB induced by a high-fat diet. It seems that the preventive effect of endurance training against obesity-related complications is partly due to the inhibition of CTSB expression in the adipose tissue.